Whitaker, 38, was one of three men awaiting execution Thursday in three different USA states.
Abbott's actions came down to the wire after an unusual move by the Texas Board of Pardons and Paroles, which recommended clemency in this case.
The Texas Tribune thanks its sponsors. None of the three were unanimous decisions by the pardons and parole board, like in Whitaker's case.
The first execution is due to take place in Florida at 6pm local time (11pm GMT).
Abbott's predecessor in the governor's office, Rick Perry, rejected two clemency recommendations for inmates facing execution and accepted one over 14 years, according to data kept by the Texas Coalition to Abolish the Death Penalty.
Rytting said Abbott should trust the parole board.
"Any time anybody's life is at stake, that's a very serious matter", Abbott told reporters at a political rally.
Whitaker was put on death row after being convicted of masterminding the deadly 2003 plot near Houston that left his mother Tricia, 51, and brother Kevin, 19, dead. Nearly two years after the crime was committed, local police received a call from Champagne which led to his confessing to the entire murder plot, revealing that Bart's roommate, Chris Brashear, was the gunman and claiming Bart had promised them millions for their assistance in the crime. "I have not granted a commutation of a death sentence until now", said Abbott, a staunch supporter of the death penalty.
The original prosecutor Fred Felcman has said he believes the decision to change the sentence has only been given based on what the father has said, rather than thinking of other victims affected by murder.
In December 2003, investigators said Whitaker arranged to make the shooting look like he and his family members interrupted a burglary as they returned home from dinner.
Kent Whitaker has told the parole board and Abbott that he'd lost all of his family except for his son, and pleaded with the state of Texas not to take him away, too. "The clock's ticking. I'm just waiting".
Bart Whitaker is on death row, convicted of the 2003 plot to kill his family. "The crime deserves severe punishment for the criminals who killed them".
In a proclamation explaining his decision, Mr Abbott wrote: "Mr Whitaker's father, who survived the attempt on his life, passionately opposes the execution of his son".
It is far more common for courts to halt executions for reasons ranging from doubts over guilt to procedural problems with prosecutions than it is for a governor to grant clemency.
Alabama, Florida and Texas plan to execute inmates on Thursday and if carried out, it would be the first time in eight years that three people on death row have been executed on the same day since the death penalty was reinstated in the United States. It would be extremely rare for the governor to go against the parole board's decision.
Whitaker could avoid execution without Abbott.
The scheduled execution for Doyle Lee Hamm, however, was delayed as the U.S. Supreme Court considers his request to block the execution.
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